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Objectives: Mitochondrial DNA (mtDNA) sequences are becoming increasingly important in the study of human population history. Here, we explore the differences in the amount of information of different mtDNA regions and their utility for the reconstruction of South American population history.
Material and methods: We analyzed six datasets comprising 259 mtDNA sequences from South America: Complete mtDNA, Coding, Control, hypervariable region I (HVRI), cytochrome b (cytb) plus Control, and cytb plus 12S plus 16S. The amount of information in each dataset was estimated employing several site-by-site and haplotype based statistics, distances among sequences, Neighbor-joining trees, distances among the estimated trees, Bayesian Skyline Plots and Phylogenetic Informativeness Profiles.
Results: The different mtDNA datasets have different amounts of information to reconstruct demographic events and phylogenetic trees with confidence. Whereas HVRI is not suitable for phylogenetic reconstruction of ancient clades, this region –as well as the Control dataset– displays information for the demographic reconstruction during the Holocene period, probably because the high rate of mutation of these regions. As expected, the Complete mtDNA and Coding region, displaying slower rate of mutation, present suitable information to estimate the founding sub-haplogroups that peopling South America and for the reconstruction of ancient demographic events.
Discussion: Our results point out the importance of evaluate the utility of different DNA regions to respond to different questions and problems in the human population studies, mainly considering the timescale of the phenomenon and the informativeness of the molecular region in a particular geographical area.
Postillone, María Bárbara and Perez, S. Ivan, "Mitochondrial-DNA Phylogenetic Information and the Reconstruction of Human Population History: The South American Case" (2017). Human Biology Open Access Pre-Prints. 126.